REAGENT or RESOURCE	SOURCE	IDENTIFIER
Bacterial and virus strains
SARS-CoV-2 strain SZ02	Shenzhen Third People’s Hospital	N/A
Biological samples
Human spleen	Xuzhou Mine Hospital	N/A
Chemicals, peptides, and recombinant proteins
Resiquimod (R848)	Sigma Aldrich	Cat# SML0196-10MG
GW9662	MedChemExpress	Cat# HY-16578
Rosiglitazone	MedChemExpress	Cat# HY-17386
Recombinant Human M-CSF	Novoprotein	Cat# C417
Glutamine	Gibco	Cat# 25030081
Sodium pyruvate	Agilent	Cat# 103578-100
2-Deoxy-D-glucose (2-DG)	Sigma	Cat# D8375
Critical commercial assays
Human TNF-α ELISA Kit	Mabtech	Cat# 3512-1H-6
Human IL-6 ELISA Kit	Mabtech	Cat# 3460-1H-6
Human MIP-1alpha (CCL3) ELISA Kit	Peprotech	Cat# 900-K35
ELISA MAX Deluxe Set Human IL-1β	Biolegend	Cat# 437004
ELISA MAX Deluxe Set Human MCP-1/CCL2	Biolegend	Cat# 438804
BODIPY™ FL C16 (4,4-Difluoro-5,7-Dimethyl-4-Bora-3a,4a-Diaza-s-Indacene-3-Hexadecanoic Acid)	Invitrogen	Cat# D3821
pHrodo™ Green E. coli BioParticles™ Conjugate for Phagocytosis	Invitrogen	Cat# P35366
SYBR qPCR Mix	Yeasen	Cat# 11198ES08
RNAiso Plus	TaKaRa	Cat# 9109
HiScript III RT SuperMix for qPCR	Vazyme	Cat# R222-01
Oligonucleotides
qPCR primers, see Table S6	This article	N/A
Software and algorithms
GraphPad Prism 8.0	GraphPad	https://www.graphpad.com/
FlowJo 10.0	Treestar	https://www.flowjo.com/solutions/flowjo
R-4.0.3	Team, 2008	https://www.r-project.org/
Seurat-3.2.2	(Stuart et al., 2019)	https://satijalab.org/seurat/
ScImpute	(Li and Li, 2018)	https://github.com/Vivianstats/scImpute
Pathway Activity	(Xiao et al., 2019)	https://github.com/LocasaleLab/Single-Cell-Metabolic-Landscape
Metascape	(Zhou et al., 2019)	https://metascape.org
Fgsea-1.16.0	(Korotkevich et al., 2021)	https://github.com/ctlab/fgsea
Monocle-2.18.0	(Trapnell et al., 2014)	http://cole-trapnell-lab.github.io/monocle-release/
Single-cell Flux Balance Analysis	(Damiani et al., 2019)	https://github.com/BIMIB-DISCo/scFBA